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- PDB-7lz4: Crystal structure of A211D mutant of Protein Kinase A RIa subunit... -

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Basic information

Entry
Database: PDB / ID: 7lz4
TitleCrystal structure of A211D mutant of Protein Kinase A RIa subunit, a Carney Complex mutation
ComponentscAMP-dependent protein kinase type I-alpha regulatory subunit, N-terminally processed
KeywordsTRANSFERASE / Carney complex / cyclic nucleotide binding domain / cyclic AMP (cAMP) / protein kinase A (PKA)
Function / homology
Function and homology information


sperm head-tail coupling apparatus / PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling / Factors involved in megakaryocyte development and platelet production / PKA activation / nucleotide-activated protein kinase complex / Hedgehog 'off' state / negative regulation of cAMP/PKA signal transduction ...sperm head-tail coupling apparatus / PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling / Factors involved in megakaryocyte development and platelet production / PKA activation / nucleotide-activated protein kinase complex / Hedgehog 'off' state / negative regulation of cAMP/PKA signal transduction / cAMP-dependent protein kinase inhibitor activity / cardiac muscle cell proliferation / sarcomere organization / cAMP-dependent protein kinase complex / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Vasopressin regulates renal water homeostasis via Aquaporins / protein kinase A catalytic subunit binding / negative regulation of activated T cell proliferation / mesoderm formation / plasma membrane raft / immunological synapse / axoneme / cAMP binding / multivesicular body / cellular response to glucagon stimulus / neuromuscular junction / positive regulation of insulin secretion / adenylate cyclase-activating G protein-coupled receptor signaling pathway / protein domain specific binding / negative regulation of gene expression / centrosome / ubiquitin protein ligase binding / glutamatergic synapse / identical protein binding / cytosol / cytoplasm
Similarity search - Function
cAMP-dependent protein kinase regulatory subunit / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / Regulatory subunit of type II PKA R-subunit / RIIalpha, Regulatory subunit portion of type II PKA R-subunit / : / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain ...cAMP-dependent protein kinase regulatory subunit / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / Regulatory subunit of type II PKA R-subunit / RIIalpha, Regulatory subunit portion of type II PKA R-subunit / : / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / RmlC-like jelly roll fold
Similarity search - Domain/homology
ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / cAMP-dependent protein kinase type I-alpha regulatory subunit
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.155 Å
AuthorsDel Rio, J. / Wu, J. / Taylor, S.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R35-GM130389 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Noncanonical protein kinase A activation by oligomerization of regulatory subunits as revealed by inherited Carney complex mutations.
Authors: Jafari, N. / Del Rio, J. / Akimoto, M. / Byun, J.A. / Boulton, S. / Moleschi, K. / Alsayyed, Y. / Swanson, P. / Huang, J. / Martinez Pomier, K. / Lee, C. / Wu, J. / Taylor, S.S. / Melacini, G.
History
DepositionMar 8, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cAMP-dependent protein kinase type I-alpha regulatory subunit, N-terminally processed
B: cAMP-dependent protein kinase type I-alpha regulatory subunit, N-terminally processed
C: cAMP-dependent protein kinase type I-alpha regulatory subunit, N-terminally processed
D: cAMP-dependent protein kinase type I-alpha regulatory subunit, N-terminally processed
E: cAMP-dependent protein kinase type I-alpha regulatory subunit, N-terminally processed
F: cAMP-dependent protein kinase type I-alpha regulatory subunit, N-terminally processed
G: cAMP-dependent protein kinase type I-alpha regulatory subunit, N-terminally processed
H: cAMP-dependent protein kinase type I-alpha regulatory subunit, N-terminally processed
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,02324
Polymers242,7568
Non-polymers5,26716
Water00
1
A: cAMP-dependent protein kinase type I-alpha regulatory subunit, N-terminally processed
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0033
Polymers30,3441
Non-polymers6582
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: cAMP-dependent protein kinase type I-alpha regulatory subunit, N-terminally processed
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0033
Polymers30,3441
Non-polymers6582
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: cAMP-dependent protein kinase type I-alpha regulatory subunit, N-terminally processed
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0033
Polymers30,3441
Non-polymers6582
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: cAMP-dependent protein kinase type I-alpha regulatory subunit, N-terminally processed
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0033
Polymers30,3441
Non-polymers6582
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: cAMP-dependent protein kinase type I-alpha regulatory subunit, N-terminally processed
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0033
Polymers30,3441
Non-polymers6582
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: cAMP-dependent protein kinase type I-alpha regulatory subunit, N-terminally processed
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0033
Polymers30,3441
Non-polymers6582
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: cAMP-dependent protein kinase type I-alpha regulatory subunit, N-terminally processed
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0033
Polymers30,3441
Non-polymers6582
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: cAMP-dependent protein kinase type I-alpha regulatory subunit, N-terminally processed
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0033
Polymers30,3441
Non-polymers6582
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)176.786, 176.786, 345.503
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq 116:299)
21chain B and (resseq 116:299)
12chain A and (resseq 317:373)
22chain B and (resseq 317:373)
13chain A and (resseq 116:299)
23chain C and (resseq 116:299)
14chain A and (resseq 317:373)
24chain C and (resseq 317:373)
15chain A and (resseq 116:299)
25chain D and (resseq 116:299)
16chain A and (resseq 317:373)
26chain D and (resseq 317:373)
17chain A and (resseq 116:299)
27chain E and (resseq 116:299)
18chain A and (resseq 317:373)
28chain E and (resseq 317:373)
19chain A and (resseq 116:299)
29chain F and (resseq 116:299)
110chain A and (resseq 317:373)
210chain F and (resseq 317:373)
111chain A and (resseq 116:299)
211chain G and (resseq 116:299)
112chain A and (resseq 317:373)
212chain G and (resseq 317:373)
113chain A and (resseq 116:299)
213chain H and (resseq 116:299)
114chain A and (resseq 317:373)
214chain H and (resseq 317:373)

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEALAALAchain A and (resseq 116:299)AA116 - 2999 - 192
21ILEILEALAALAchain B and (resseq 116:299)BB116 - 2999 - 192
12GLYGLYSERSERchain A and (resseq 317:373)AA317 - 373210 - 266
22GLYGLYSERSERchain B and (resseq 317:373)BB317 - 373210 - 266
13ILEILEALAALAchain A and (resseq 116:299)AA116 - 2999 - 192
23ILEILEALAALAchain C and (resseq 116:299)CC116 - 2999 - 192
14GLYGLYSERSERchain A and (resseq 317:373)AA317 - 373210 - 266
24GLYGLYSERSERchain C and (resseq 317:373)CC317 - 373210 - 266
15ILEILEALAALAchain A and (resseq 116:299)AA116 - 2999 - 192
25ILEILEALAALAchain D and (resseq 116:299)DD116 - 2999 - 192
16GLYGLYSERSERchain A and (resseq 317:373)AA317 - 373210 - 266
26GLYGLYSERSERchain D and (resseq 317:373)DD317 - 373210 - 266
17ILEILEALAALAchain A and (resseq 116:299)AA116 - 2999 - 192
27ILEILEALAALAchain E and (resseq 116:299)EE116 - 2999 - 192
18GLYGLYSERSERchain A and (resseq 317:373)AA317 - 373210 - 266
28GLYGLYSERSERchain E and (resseq 317:373)EE317 - 373210 - 266
19ILEILEALAALAchain A and (resseq 116:299)AA116 - 2999 - 192
29ILEILEALAALAchain F and (resseq 116:299)FF116 - 2999 - 192
110GLYGLYSERSERchain A and (resseq 317:373)AA317 - 373210 - 266
210GLYGLYSERSERchain F and (resseq 317:373)FF317 - 373210 - 266
111ILEILEALAALAchain A and (resseq 116:299)AA116 - 2999 - 192
211ILEILEALAALAchain G and (resseq 116:299)GG116 - 2999 - 192
112GLYGLYSERSERchain A and (resseq 317:373)AA317 - 373210 - 266
212GLYGLYSERSERchain G and (resseq 317:373)GG317 - 373210 - 266
113ILEILEALAALAchain A and (resseq 116:299)AA116 - 2999 - 192
213ILEILEALAALAchain H and (resseq 116:299)HH116 - 2999 - 192
114GLYGLYSERSERchain A and (resseq 317:373)AA317 - 373210 - 266
214GLYGLYSERSERchain H and (resseq 317:373)HH317 - 373210 - 266

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14

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Components

#1: Protein
cAMP-dependent protein kinase type I-alpha regulatory subunit, N-terminally processed


Mass: 30344.449 Da / Num. of mol.: 8 / Mutation: A211D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: PRKAR1A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00514
#2: Chemical
ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP


Mass: 329.206 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C10H12N5O6P / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.29 Å3/Da / Density % sol: 71.32 % / Description: Four individual dimers per asymmetrical unit
Crystal growTemperature: 295.5 K / Method: vapor diffusion, hanging drop / pH: 5
Details: The protein was concentrated to 8 mg/mL, and crystallized in 2 uL hanging drops using the vapor diffusion method with 75 mM Sodium Acetate (pH 5.0), 2.0 M sodium formate, and four-fold molar ...Details: The protein was concentrated to 8 mg/mL, and crystallized in 2 uL hanging drops using the vapor diffusion method with 75 mM Sodium Acetate (pH 5.0), 2.0 M sodium formate, and four-fold molar excess cAMP at room temperature
Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.15→50 Å / Num. obs: 30356 / % possible obs: 99.3 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 12.8
Reflection shellResolution: 4.15→4.22 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1504 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.7_650refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RGS

1rgs


Resolution: 4.155→48.249 Å / SU ML: 0.59 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 29.74 / Stereochemistry target values: ML
Details: noncrystallographic symmetry restraints using Phenix.
RfactorNum. reflection% reflection
Rfree0.2699 1524 5.06 %
Rwork0.221 28613 -
obs0.2239 30137 99.27 %
Solvent computationShrinkage radii: 0.04 Å / VDW probe radii: 0.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 123.591 Å2 / ksol: 0.384 e/Å3
Displacement parametersBiso max: 318.99 Å2 / Biso mean: 145.81 Å2 / Biso min: 2.61 Å2
Baniso -1Baniso -2Baniso -3
1-5.5175 Å20 Å2-0 Å2
2--5.5175 Å20 Å2
3----11.035 Å2
Refinement stepCycle: final / Resolution: 4.155→48.249 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16786 0 352 0 17138
Biso mean--133.12 --
Num. residues----2142
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02920668
X-RAY DIFFRACTIONf_angle_d3.2627983
X-RAY DIFFRACTIONf_chiral_restr0.2093082
X-RAY DIFFRACTIONf_plane_restr0.0153602
X-RAY DIFFRACTIONf_dihedral_angle_d22.9497838
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1454X-RAY DIFFRACTIONPOSITIONAL0.202
12B1454X-RAY DIFFRACTIONPOSITIONAL0.202
21A450X-RAY DIFFRACTIONPOSITIONAL0.144
22B450X-RAY DIFFRACTIONPOSITIONAL0.144
31A1454X-RAY DIFFRACTIONPOSITIONAL0.199
32C1454X-RAY DIFFRACTIONPOSITIONAL0.199
41A450X-RAY DIFFRACTIONPOSITIONAL0.166
42C450X-RAY DIFFRACTIONPOSITIONAL0.166
51A1454X-RAY DIFFRACTIONPOSITIONAL0.198
52D1454X-RAY DIFFRACTIONPOSITIONAL0.198
61A450X-RAY DIFFRACTIONPOSITIONAL0.224
62D450X-RAY DIFFRACTIONPOSITIONAL0.224
71A1454X-RAY DIFFRACTIONPOSITIONAL0.18
72E1454X-RAY DIFFRACTIONPOSITIONAL0.18
81A450X-RAY DIFFRACTIONPOSITIONAL0.166
82E450X-RAY DIFFRACTIONPOSITIONAL0.166
91A1454X-RAY DIFFRACTIONPOSITIONAL0.218
92F1454X-RAY DIFFRACTIONPOSITIONAL0.218
101A450X-RAY DIFFRACTIONPOSITIONAL0.136
102F450X-RAY DIFFRACTIONPOSITIONAL0.136
111A1454X-RAY DIFFRACTIONPOSITIONAL0.211
112G1454X-RAY DIFFRACTIONPOSITIONAL0.211
121A450X-RAY DIFFRACTIONPOSITIONAL0.139
122G450X-RAY DIFFRACTIONPOSITIONAL0.139
131A1454X-RAY DIFFRACTIONPOSITIONAL0.161
132H1454X-RAY DIFFRACTIONPOSITIONAL0.161
141A450X-RAY DIFFRACTIONPOSITIONAL0.14
142H450X-RAY DIFFRACTIONPOSITIONAL0.14
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
4.155-4.28870.35071280.2547253897
4.2887-4.44190.33771490.24762617100
4.4419-4.61960.26931460.1833256699
4.6196-4.82970.25991320.1586260299
4.8297-5.0840.25381400.15672609100
5.084-5.40220.26561400.18532598100
5.4022-5.81860.3141270.21482631100
5.8186-6.4030.29951150.20832637100
6.403-7.32670.26721380.19662630100
7.3267-9.22030.26551590.1882590100
9.2203-48.2490.32191500.3023259599

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